Protein folding

Question 1

do all the stages of replication need to be error free for proteins to work

Answer 1

yes

DNA needs to be without mutations that change the code
RNA needs to be properly transcribed without error
Protein need to be translated, folded and located in the correct part of the cell or outside it

Question 2

what type of RNA binds each triplet of RNA bases

Answer 2

tRNA

Question 3

what is the primary structure of proteins

Answer 3

linear sequence of amino-acids residues in the polypeptide chain
e.g. insulin has 2

Question 4

what is the secondary structure of proteins

Answer 4

local folded structures
between atoms of backbone
most common structures are folding of alpha helix and beta bleated sheets

backbone

Question 5

what type of bond holds beta pleated sheets and alpha helixes together

Answer 5

hydrogen bonds

pull on electrons and partial negative and partial positive charges causing folds and swirls

Question 6

what is the tertiary structure of a protein

Answer 6

3D structure due to interactions between R groups of the amino acids that make up the protein
ionic bonds, polar forces , hydrophobic ( inside ) and hydrophilic , London dispersion forces and dipole and dipole
disulphide bonds - cysteine strongest

chain interactions

Question 7

what is the quaternary structure of a protein

Answer 7

multiple polypeptide chains - also know as subunits

e.g. Hb -4 subunits alpha and beta

Question 8

what process Is essential to move proteins to the right place on the membrane

Answer 8

protein translocation into the endoplasmic reticulum

Question 9

how do membrane proteins enter membrane at the endoplasmic reticulum

Answer 9

signal recognition particle ( SRP) binds to newly synthesised peptide pausing protein synthesis.
until complex find SRP receptor on ER membrane. UPon docking the new peptide chain is inserted into the translocation channel. Protein synthesis will resume once SRP has been released from the ribosome.

Question 10

5 steps of CFTR synthesis

Answer 10

Transcription 
Translation and protein folding 
post-translational modification at the Golgi
protein trafficking 
surface expression of CFTR

Question 11

what is this idea of quality control

Answer 11

not all protein may get to membrane or may not work when they get there due to cell having inbuilt system to deal with misfolded proteins

Question 12

where does the control process fro CFTR happen

Answer 12

ER

Question 13

if a protein is misfolded is it salvageable

Answer 13

yes can be refolded by chaperone proteins in the ER
However if a protein is terminally misfolded it is passed back through the ER membrane ( retrotranslocation ) into the cytoplasm where it is degraded by protease enzymes
two fates - recycled back or targeted foo degradation

Question 14

How many classes of cystic fibrosis folding problems are there?

Answer 14

6

Question 15

what is a class 1 CFTR protein mutation

Answer 15

nonsense( premature stop) mutation so a truncation mutation which means no functional protein is made so no CFTR protein

Question 16

what is a class 2 CFTR protein mutation

Answer 16

missense mutation and the CFTR protein has become misfiled so it can’t traffic through the endoplasmic reticulum through the golgi to the cell membrane so it becomes degraded (substitution)(amino acid deletion)

Question 17

example of a class 2 mutation

Answer 17

Phe508del

Question 18

what is a class 3 CFTR protein mutation

Answer 18

protein gets to the cell membrane but docent function and won’t transport chloride ions - defective channel regulation
missense ( aa change)

Question 19

example of a class 3 mutation

Answer 19

Gly551Asp

Question 20

what is a class 4 CFTR mutation

Answer 20

protein dosent fiction at cell membrane due to decreased channel conductance
missence aa change

Question 21

what is a class 5 CFTR protein mutation

Answer 21

only small amounts of proteins getting to the cell membrane so not much CFTR at the cell membrane to transport chloride
splicing defect - missence

Question 22

what is a class 6 CFTR protein mutation

Answer 22

protein gets to the cell membrane but it isn’t stable so it is quickly endocytose back into the cell and degraded
missence and aa change

Question 23

what is the most prevalent class mutation

Answer 23

2

Question 24

if I was to try and treat class 3 and 4 mutations what type of drug would I give and an example of this

Answer 24

potentiators

e.g. ivacaftor

Question 25

how could we treat a class 2 mutation

Answer 25

using a corrector such as lumacaftor with a potentiator ( ivacaftor)

Question 26

Severe genotypes of CFTR include patients who are homozygous (both genes have the same mutation) or compound heterozygous (the genes are different but both classed as severe genotypes) for what types of mutations

Answer 26

class I, II, III mutations.

Question 27

what is p.Phe508del mutation what happens to the protein

Answer 27

deletion of 3 DNA bases resulting in a missing phenylalanine (F) amino acid at position 508 in the protein so protein dosent fold properly This misfolded CFTR is recognised by the cell’s quality control machinery and held in the ER and is then degraded p.Phe508del can't perform its function (as it doesn’t reach the plasma membrane of the cell) and this results in the symptoms of CF

Question 28

what is the p.Gly551Asp mutation

Answer 28

``` Most common CFTR gating (class III) mutation, present in 4% of patients with CF single nucleotide variant The protein gets to the cell membrane but it doesn’t function very well. ``` Result in the production of a CFTR protein that makes it to the cell membrane but does not open correctly. “gating defect.”

Question 29

examples of chaperone( conformational folding or unfolding of proteins) proteins

Answer 29

Bip and calnexin | both in ER

Question 30

Ubiquitin function

Answer 30

small protein found in almost all cellular tissues regulates processes of other proteins - tagged fro degradation proteasome degrades it

Question 31

Treatment for CF - limited to targeting the secondary effects of he defective CFTR protein

Answer 31

``` Broncho diators, antibiotics and corticosteroids Pulmozyme , insulin and bisphosphates Vaccinations and flu jabs Enzymes , diet and nutrition Physiotherapy , airway clearance Lung transplantation ```

Question 32

what classes do potentiator drugs help

Answer 32

3 and 4 the rest need correctors and mixture

Question 33

what do potentiators do

Answer 33

increase the activity of defective CFTR at the cell surface. They either act on gating or conductance defects ( i.e. if gating enhanced opening and if conductance defect increase he flow of ions through CFTR) regulating amount of fluids at the surface of the cell

Question 34

what do correctors do

Answer 34

overcome defective protein processing that normally result in the production of misfolded CFTR. This allows increased trafficking of CFTR to the plasma membrane correctors increase the surface density of CFTR at the membrane. They may also enhance the function of CFTR at the membrane

Question 35

what are production correctors

Answer 35

these instruct the ribosomes to read through premature termination codons ( PTCs) during mRNA translation - these are for the ones when non proteins are made read through agent promote the read through of premature termination codons in CFTR mRNA the right stop codon is reached so a complete CFTR polypeptide is made and translated

Question 36

what does ivacaftor/kaleydeco do

Answer 36

increase opening time of the channel for type 3 and 4

Question 37

what were some of the clinical effects of ivacaftor in patients with at least one class 3 CFTR mutation

Answer 37

Increase ( approx 10% ) in FEV1 ( lung function) Weight gain ( approx 2.8kg) Decreased pulmonary exacerbations ( approx 50%) Decreased sweat chloride concentration Decreased endobronchial colonization with P.aeruginosa

Question 38

what is a QALY

Answer 38

quality-adjusted life year - assess value of medical interventions

Question 39

what percentage of people have class 3 mutation ?

Answer 39

3.9%

Question 40

what do correctors increase

Answer 40

the surface density of CFTR at the membrane - may also enhance the function of CFTR at the membrane

Question 41

what is orkambi | what effects did it have

Answer 41

ivacaftor/lumicaftor Reduced pulmonary exacerbations Increased BMI Increased FEV1 - lung capacity given over the age of 2 Lumicaftor in orkambi - induces enzyme that metabolises the ivacaftor drug so reducing that amount available Tezacaftor - corrector - alternative corrector - symkevi - over age of 12 with that mutation or one of those functions

Question 42

what drugs are involved in the triple combination therapy of CF

Answer 42

elexacaftor, tezacaftor and ivacaftor 2correctors

Question 43

membrane proteins fold at the ER through the what

Answer 43

translocon

Question 44

what other incurable diseases are caused by protein msifolding/aggregation

Answer 44

alzeihmers parkinsons huntigntons amyotrophic lateral sclerosis

Question 45

what things help inform new medicine for folding disease

Answer 45

computer simulations(predictions can be made on how they fold ) , cell biology and structural studies

Question 46

ACH inhibitors can help Alzheimers true or false ?

Answer 46

true